Thank you for the response! Below is the command line I used:
mri_vol2surf --srcsubject Tract_HC_001_07222016 --hemi lh --projopt /autofs/space/allegro_002/users/hlee/SANDI/pvf/Tract_HC_001_07222016/pvf --projfrac 0 --surf white --srcreg /autofs/space/rhapsody_001/users/Bay8_C1/bids/derivatives/supres/sub-001/bbr/diff_bbr_t1w.dat --src /autofs/cluster/connectome2/Bay8_C1/bids/derivatives/SANDI/supres/sub-001/sub-001-SANDI-fit_De.nii.gz --out /autofs/cluster/connectome2/Bay8_C1/bids/derivatives/SANDI/supres/surf_pvf/sub-001/lh.De.100.overlay.mgz –cortex I have the following files pvf.gm.mgz, pvf.wm.mgz, pvf.csf.mgz, and pvf.subcort_gm.mgz in the directory: /autofs/space/allegro_002/users/hlee/SANDI/pvf/Tract_HC_001_07222016. Please let me know if you need additional details. Thanks! Hansol From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@mgh.harvard.edu> Date: Tuesday, November 12, 2024 at 10:55 AM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_vol2surf error: GM estimation couldn't find enough samples what is your command line? On 11/11/2024 3:47 PM, Lee, Hansol wrote: Dear FreeSurfer developers, I am attempting to use “mri_vol2surf” command to project output from diffusion MRI models (e.g., DTI) onto the cortical surface. The registration between the diffusion MRI and anatomical space was performed using “bbregister”, and the projection works well for different --projfrac values (e.g., 0 to 1 from the white matter surface). However, I encountered issues when attempting to use the “—projopt” option to account for partial volume effects. Specifically, I received the following errors: “reading gm volume fraction from /autofs/space/allegro_002/users/hlee/SANDI/pvf/Tract_HC_001_07222016/pvf.gm.mgz reading wm volume fraction from /autofs/space/allegro_002/users/hlee/SANDI/pvf/Tract_HC_001_07222016/pvf.wm.mgz reading csf volume fraction from /autofs/space/allegro_002/users/hlee/SANDI/pvf/Tract_HC_001_07222016/pvf.csf.mgz error: No such file or directory error: GM estimation at vno 0 couldn't find enough samples error: No such file or directory error: GM estimation at vno 1 couldn't find enough samples error: No such file or directory error: GM estimation at vno 2 couldn't find enough samples error: No such file or directory error: GM estimation at vno 3 couldn't find enough samples error: No such file or directory error: GM estimation at vno 4 couldn't find enough samples error: No such file or directory error: GM estimation at vno 5 couldn't find enough samples error: No such file or directory” In the directory, I already have “pvf.gm.mgz”, “pvf.wm.mgz”, and “pvf.csf.mgz” files. I searched the archive and found a similar error reported in this thread: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg72784.html I would greatly appreciate any insights or suggestions to resolve this issue. Thank you in advance for your help! Best regards, Hansol Lee _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
